Align SmoF, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate GFF1304 PGA1_c13200 ABC transporter permease protein
Query= TCDB::O30832 (290 letters) >FitnessBrowser__Phaeo:GFF1304 Length = 288 Score = 374 bits (960), Expect = e-108 Identities = 193/290 (66%), Positives = 237/290 (81%), Gaps = 2/290 (0%) Query: 1 MATQHSKTAARLMISPAVILLFLWMIVPLSMTLYFSFLRYNLLMPGMESFTGWDNYYYFL 60 MATQHS++AAR+M++PAVILL WM+VPL+MTLYFSF +Y L G + G+DNY FL Sbjct: 1 MATQHSRSAARIMMAPAVILLLGWMLVPLTMTLYFSFKKYLPLRGGDLGWVGFDNYARFL 60 Query: 61 TDPAFSAALTNTILLVVGVLLITVVGGVLLALLLDQPFWGQGIVRVLVIAPFFVMPTVSA 120 + AF ++ T+++V GVL ITV+ GV LALLL+QP WGQGIVR+LVIAPFFVMPTVSA Sbjct: 61 SSSAFWPSVQATLVIVGGVLAITVILGVFLALLLNQPMWGQGIVRILVIAPFFVMPTVSA 120 Query: 121 LVWKNMFMNPVNGMFAHIARGLGLPPFDFLSQAPLASIIGIVAWQWLPFATLILLTALQS 180 LVWKNMFM+PVNG+FAH+ + G P +LS+A L SII IV+WQWLPFATLILLTA+QS Sbjct: 121 LVWKNMFMDPVNGLFAHLWKAFGAEPVSWLSEASLQSIILIVSWQWLPFATLILLTAIQS 180 Query: 181 LDREQMEAAEMDGASALDRFIHITVPHLTRAITVVVLIQTIFLLGVFAEILVTTNGGPGT 240 LD EQ+EAAEMDGA + RF +IT+PHL+RAITVVVLIQTIFLL +FAEI VTT G GT Sbjct: 181 LDSEQLEAAEMDGAPPVARFGYITLPHLSRAITVVVLIQTIFLLSIFAEIFVTTQGSFGT 240 Query: 241 ASTNITYLVYAQSLLNYDVGGGSAGGIVAVVLANIVAIFLMRMIGKNLDA 290 + +TYL+Y + L + +VG GSAGG+ A++LANIVAIFLMR++GKNLDA Sbjct: 241 KT--LTYLIYQRVLESQNVGLGSAGGVYAIILANIVAIFLMRIVGKNLDA 288 Lambda K H 0.329 0.142 0.429 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 303 Number of extensions: 7 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 290 Length of database: 288 Length adjustment: 26 Effective length of query: 264 Effective length of database: 262 Effective search space: 69168 Effective search space used: 69168 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory